+Open data
-Basic information
Entry | Database: PDB / ID: 3frr | ||||||
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Title | Structure of human IST1(NTD) - (residues 1-189)(P21) | ||||||
Components | Uncharacterized protein KIAA0174 | ||||||
Keywords | PROTEIN BINDING / ESCRT / ESCRT-III / CHMP / IST1 / Alternative splicing / Phosphoprotein | ||||||
Function / homology | Function and homology information viral capsid secondary envelopment / MIT domain binding / abscission / ESCRT III complex disassembly / cytoskeleton-dependent cytokinesis / collateral sprouting / Sealing of the nuclear envelope (NE) by ESCRT-III / positive regulation of collateral sprouting / multivesicular body assembly / Flemming body ...viral capsid secondary envelopment / MIT domain binding / abscission / ESCRT III complex disassembly / cytoskeleton-dependent cytokinesis / collateral sprouting / Sealing of the nuclear envelope (NE) by ESCRT-III / positive regulation of collateral sprouting / multivesicular body assembly / Flemming body / positive regulation of proteolysis / endoplasmic reticulum-Golgi intermediate compartment / viral release from host cell / establishment of protein localization / protein localization / azurophil granule lumen / protein transport / nuclear envelope / midbody / cadherin binding / protein domain specific binding / cell division / intracellular membrane-bounded organelle / centrosome / Neutrophil degranulation / chromatin / protein-containing complex binding / extracellular exosome / extracellular region / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å | ||||||
Authors | Schubert, H.L. / Hill, C.P. / Bajorek, M. / Sundquist, W.I. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2009 Title: Structural basis for ESCRT-III protein autoinhibition. Authors: Bajorek, M. / Schubert, H.L. / McCullough, J. / Langelier, C. / Eckert, D.M. / Stubblefield, W.M. / Uter, N.T. / Myszka, D.G. / Hill, C.P. / Sundquist, W.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3frr.cif.gz | 55.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3frr.ent.gz | 39.1 KB | Display | PDB format |
PDBx/mmJSON format | 3frr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3frr_validation.pdf.gz | 423.1 KB | Display | wwPDB validaton report |
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Full document | 3frr_full_validation.pdf.gz | 423.5 KB | Display | |
Data in XML | 3frr_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | 3frr_validation.cif.gz | 14.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fr/3frr ftp://data.pdbj.org/pub/pdb/validation_reports/fr/3frr | HTTPS FTP |
-Related structure data
Related structure data | 3frsC 3frtC 3frvC 2gd5S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 21769.480 Da / Num. of mol.: 1 / Fragment: UNP residues 1-189 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IST1, KIAA0174 / Plasmid: pGST / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Codon+RIL / References: UniProt: P53990 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.94 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7.6 Details: 35% pentaethritol propexylate 180mM KCl 50 mM HEPES, pH 7.6 7% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 11, 2008 |
Radiation | Monochromator: Verimax HR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 15886 / Num. obs: 15886 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 25.4 Å2 / Rmerge(I) obs: 0.053 / Χ2: 1.056 / Net I/σ(I): 19.209 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.163 / Mean I/σ(I) obs: 4.5 / Num. unique all: 1296 / Χ2: 1.001 / % possible all: 79.1 |
-Phasing
Phasing | Method: molecular replacement |
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Phasing MR | Model details: Phaser MODE: MR_AUTO |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2GD5 Resolution: 1.8→46.18 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.271 / WRfactor Rwork: 0.214 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.817 / SU B: 3.242 / SU ML: 0.103 / SU R Cruickshank DPI: 0.162 / SU Rfree: 0.153 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 70.02 Å2 / Biso mean: 27.235 Å2 / Biso min: 8.17 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→46.18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.844 Å / Total num. of bins used: 20
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